Calcium in PDB 4mkf: Crystal Structure of A Stable Adenylate Kinase Variant AKV3
Enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKV3
All present enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKV3:
2.7.4.3;
Protein crystallography data
The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKV3, PDB code: 4mkf
was solved by
S.Moon,
D.Jung,
E.Bae,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
26.99 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
34.447,
75.008,
77.195,
90.00,
100.89,
90.00
|
R / Rfree (%)
|
15.7 /
20.3
|
Other elements in 4mkf:
The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3
(pdb code 4mkf). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Crystal Structure of A Stable Adenylate Kinase Variant AKV3, PDB code: 4mkf:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 4mkf
Go back to
Calcium Binding Sites List in 4mkf
Calcium binding site 1 out
of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca304
b:34.1
occ:1.00
|
OE1
|
A:GLN199
|
2.3
|
20.1
|
1.0
|
O
|
A:HOH459
|
2.5
|
25.2
|
1.0
|
O
|
A:HOH585
|
2.6
|
30.9
|
1.0
|
CD
|
A:GLN199
|
3.5
|
19.2
|
1.0
|
NE2
|
A:GLN199
|
4.3
|
15.9
|
1.0
|
O
|
A:HOH499
|
4.4
|
37.8
|
1.0
|
CG
|
A:GLN199
|
4.5
|
18.6
|
1.0
|
OD2
|
A:ASP207
|
4.6
|
16.0
|
1.0
|
OD1
|
A:ASP207
|
4.8
|
18.0
|
1.0
|
CB
|
A:ASP203
|
4.8
|
18.4
|
1.0
|
|
Calcium binding site 2 out
of 7 in 4mkf
Go back to
Calcium Binding Sites List in 4mkf
Calcium binding site 2 out
of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca305
b:28.1
occ:1.00
|
O
|
A:HOH628
|
2.2
|
25.7
|
1.0
|
O
|
A:HOH629
|
2.2
|
30.7
|
1.0
|
OD1
|
A:ASP203
|
2.3
|
23.6
|
1.0
|
OD2
|
A:ASP203
|
2.8
|
23.4
|
1.0
|
CG
|
A:ASP203
|
2.9
|
22.9
|
1.0
|
CB
|
A:ASP203
|
4.4
|
18.4
|
1.0
|
OD2
|
A:ASP200
|
4.9
|
31.3
|
1.0
|
|
Calcium binding site 3 out
of 7 in 4mkf
Go back to
Calcium Binding Sites List in 4mkf
Calcium binding site 3 out
of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca306
b:25.0
occ:1.00
|
O
|
A:HOH624
|
2.3
|
15.2
|
1.0
|
O
|
A:HOH517
|
2.3
|
19.9
|
1.0
|
O
|
A:GLY73
|
2.3
|
19.1
|
1.0
|
O
|
A:HOH519
|
2.6
|
29.3
|
1.0
|
O
|
A:HOH591
|
2.7
|
35.2
|
1.0
|
C
|
A:GLY73
|
3.5
|
18.7
|
1.0
|
O
|
A:HOH473
|
4.2
|
37.4
|
1.0
|
CA
|
A:GLY73
|
4.2
|
18.1
|
1.0
|
N
|
A:LYS74
|
4.4
|
17.7
|
1.0
|
O
|
A:HOH538
|
4.5
|
22.2
|
1.0
|
O
|
A:HOH604
|
4.5
|
34.7
|
1.0
|
CA
|
A:LYS74
|
4.5
|
17.7
|
1.0
|
C
|
A:LYS74
|
5.0
|
16.0
|
1.0
|
|
Calcium binding site 4 out
of 7 in 4mkf
Go back to
Calcium Binding Sites List in 4mkf
Calcium binding site 4 out
of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca304
b:13.3
occ:1.00
|
O
|
B:HOH627
|
2.4
|
13.8
|
1.0
|
O
|
B:HOH631
|
2.4
|
12.8
|
1.0
|
O
|
B:HOH628
|
2.4
|
12.9
|
1.0
|
OD2
|
B:ASP200
|
2.4
|
14.8
|
1.0
|
O
|
B:HOH629
|
2.5
|
14.5
|
1.0
|
O
|
B:HOH630
|
2.5
|
14.7
|
1.0
|
CG
|
B:ASP200
|
3.4
|
14.7
|
1.0
|
CB
|
B:ASP200
|
3.7
|
13.2
|
1.0
|
O
|
B:HOH588
|
4.2
|
27.1
|
1.0
|
OD2
|
B:ASP203
|
4.3
|
13.9
|
1.0
|
OD1
|
B:ASP200
|
4.5
|
14.6
|
1.0
|
OE1
|
B:GLU202
|
4.5
|
17.9
|
1.0
|
CA
|
B:CA305
|
4.6
|
21.4
|
1.0
|
OD1
|
B:ASP203
|
4.8
|
13.9
|
1.0
|
CG
|
B:ASP203
|
4.8
|
13.2
|
1.0
|
|
Calcium binding site 5 out
of 7 in 4mkf
Go back to
Calcium Binding Sites List in 4mkf
Calcium binding site 5 out
of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca305
b:21.4
occ:1.00
|
O
|
B:HOH473
|
2.3
|
29.6
|
1.0
|
O
|
B:HOH636
|
2.4
|
36.5
|
1.0
|
OD1
|
B:ASP200
|
2.4
|
14.6
|
1.0
|
O
|
B:HOH588
|
2.5
|
27.1
|
1.0
|
O
|
B:HOH592
|
2.5
|
27.5
|
1.0
|
OD2
|
B:ASP200
|
2.6
|
14.8
|
1.0
|
O
|
B:HOH402
|
2.6
|
24.7
|
1.0
|
CG
|
B:ASP200
|
2.9
|
14.7
|
1.0
|
O
|
B:HOH554
|
4.3
|
25.7
|
1.0
|
CB
|
B:ASP200
|
4.4
|
13.2
|
1.0
|
O
|
B:HOH630
|
4.5
|
14.7
|
1.0
|
CA
|
B:CA304
|
4.6
|
13.3
|
1.0
|
O
|
B:HOH581
|
4.7
|
14.9
|
1.0
|
O
|
B:HOH631
|
4.7
|
12.8
|
1.0
|
O
|
B:HOH628
|
4.9
|
12.9
|
1.0
|
|
Calcium binding site 6 out
of 7 in 4mkf
Go back to
Calcium Binding Sites List in 4mkf
Calcium binding site 6 out
of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca306
b:14.1
occ:1.00
|
OE1
|
B:GLN199
|
2.2
|
12.4
|
1.0
|
O
|
B:HOH587
|
2.3
|
17.9
|
1.0
|
O
|
B:HOH613
|
2.4
|
12.8
|
1.0
|
O
|
B:HOH614
|
2.5
|
16.3
|
1.0
|
CD
|
B:GLN199
|
3.4
|
11.5
|
1.0
|
NE2
|
B:GLN199
|
4.0
|
11.1
|
1.0
|
O
|
B:HOH549
|
4.3
|
31.9
|
1.0
|
OD1
|
B:ASP207
|
4.3
|
13.5
|
1.0
|
CB
|
B:ASP203
|
4.5
|
12.4
|
1.0
|
CG
|
B:GLN199
|
4.5
|
11.7
|
1.0
|
OD2
|
B:ASP207
|
4.5
|
13.7
|
1.0
|
O
|
B:ASP203
|
4.6
|
11.5
|
1.0
|
CG
|
B:ASP207
|
4.9
|
13.0
|
1.0
|
|
Calcium binding site 7 out
of 7 in 4mkf
Go back to
Calcium Binding Sites List in 4mkf
Calcium binding site 7 out
of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca307
b:13.3
occ:1.00
|
O
|
B:HOH625
|
2.3
|
13.0
|
1.0
|
O
|
A:HOH617
|
2.4
|
16.9
|
1.0
|
O
|
B:HOH626
|
2.4
|
13.6
|
1.0
|
O
|
B:LYS40
|
2.4
|
13.1
|
1.0
|
O
|
B:HOH495
|
2.4
|
20.2
|
1.0
|
O
|
A:HOH436
|
2.5
|
17.3
|
1.0
|
O
|
B:HOH586
|
2.6
|
19.0
|
1.0
|
C
|
B:LYS40
|
3.5
|
14.6
|
1.0
|
CA
|
B:LYS40
|
4.0
|
14.2
|
1.0
|
OE2
|
B:GLU42
|
4.0
|
18.3
|
1.0
|
CG
|
B:LYS40
|
4.3
|
20.0
|
1.0
|
O
|
A:LEU215
|
4.3
|
20.8
|
1.0
|
N
|
A:MET1
|
4.3
|
13.6
|
1.0
|
CG
|
B:GLU42
|
4.4
|
15.3
|
1.0
|
OD2
|
A:ASP108
|
4.4
|
12.6
|
1.0
|
O
|
A:HOH502
|
4.4
|
36.0
|
1.0
|
OD1
|
A:ASP108
|
4.5
|
13.5
|
1.0
|
O
|
B:MET39
|
4.6
|
12.2
|
1.0
|
N
|
B:GLU41
|
4.7
|
14.2
|
1.0
|
CD
|
B:GLU42
|
4.7
|
16.9
|
1.0
|
CB
|
B:LYS40
|
4.8
|
17.0
|
1.0
|
O
|
B:HOH560
|
4.8
|
35.6
|
1.0
|
CG
|
A:ASP108
|
4.9
|
12.0
|
1.0
|
O
|
B:HOH536
|
4.9
|
37.6
|
1.0
|
|
Reference:
S.Moon,
D.Jung,
G.N.Phillips,
E.Bae.
An Integrated Approach For Thermal Stabilization of A Mesophilic Adenylate Kinase Proteins 2014.
ISSN: ESSN 1097-0134
PubMed: 24615904
DOI: 10.1002/PROT.24549
Page generated: Sun Jul 14 10:25:36 2024
|